Chromophores definition

Z- E configurational change of the chromophore and the subsequent conformational changes of the protein [63]. However, in view of the considerable uncertainties about the size of the orientation angles and about the conformations of the Pr and Pfr chromophores, definitive conclusions on this point would be premature at the present. 

The art of developing a good CD model thus lies totally in the chromophore definitions, a factor usually swamped by complex perturbation expressions. The importance of this point cannot be overstressed, as the failure of some CD models stems ultimately from an oversimplified chromophore definition, a deficiency that, in most cases, cannot be remedied by any subsequent theoretical refinements (e.g. going to higher order in perturbation theory). 

No definitive evidence has appeared that identifies the source of the color generated duriag thermooxidatioa (95). However, two laboratories have postulated that the reactioas leading to the formation of the color chromophores are aldol-type reactioas, either via the reactioa of aldehydes direedy (96)... 

It can be seen from Figures 3.7 and 3.8 that the calculations reproduce very well not only the experimental spectra but also the experimentally observed isotopic shifts indicating a high reliability of the computational method. According to this comparison, definite attribution can be made for even the difficult Raman bands that cannot be assigned based solely on the experimental results. It is, however, necessary to mention at this point that the calculated Raman spectrum provided directly by the ab initio computations correspond to the normal Raman spectrum with the band intensity determined by the polarizability of the correlating vibration. Since the intensity pattern exhibited by the experimentally recorded resonance Raman spectrum is due to the resonance enhancement effect of a particular chromophore, with no consideration of this effect, the calculated intensity pattern may, in many... 

Another, very notable, case where the two definitions are in conflict is that of het-eroannular cisoid dienes. As we have mentioned, this was just the class of molecules that stimulated the introduction of the AAR. Here, in order to have the correct results one should refer the chirality of the axial substituent to the individual double bonds (olefin-picture), as depicted in Figure 6 and in the upper parts of Figure 7(b) and (c). The case of heteroannular dienes is anyway peculiar, because in these compounds the chromophore is unusually distorted. This case is treated in the following section. 

Within the mixed quantum/classical approach, at each time step in a classical molecular dynamics simulation (that is, for each configuration of the bath coordinates), for each chromophore one needs the transition frequency and the transition dipole or polarizability, and if there are multiple chromophores, one needs the coupling frequencies between each pair. For water a number of different possible approaches have been used to obtain these quantities in this section we begin with brief discussions of each approach to determine transition frequencies. For definiteness we consider the case of a single OH stretch chromophore on an HOD molecule in liquid D2O. 

Most chromophores absorb light along a preferred direction1 (see Chapter 2 for the definition of absorption transition moment, and for examples of transition moments of some fluorophores, see Figure 2.3), depending on the electronic state. In contrast, the emission transition moment is the same whatever the excited state reached by the molecule upon excitation, because of internal conversion towards the first singlet state (Figure 5.2). 

In several examples including nitroanilines, the effect of twisting the chromophore from planarity decreases the absorption intensities. The reasons for the bathochromic effect as the angles of twist in the 4-aniline series increase is subject to discussion. When considering this (as well as in all attempts to obtain definitions of polarity of solvents by quantitative parameters) it is important to exclude or minimize the presence of hydrogen bonding overlapping158 other interactions. 

More definite evidence for the transient existence of the un-cyclized l-(jS-aminoethyl)-3,4-benzoquinones has been obtained recently by Kodja and Bouchilloux,77 78 who noted that a transient yellow color (Amax ca. 385 mp) was occasionally observed during the enzymic oxidations of catecholamines (particularly in unbuffered systems at low temperatures). This phenomenon was probably due to the formation of the transient o-quinones. (The absorption maximum of o-benzoquinone, the effective chromophore of the open-chain quinones, is known to occur at ca. 390 mp.79) An absorption maximum at 390 mp is characteristic of the formation of the dopa-quinone chromophore during oxidation of small C -terminal tyrosine peptides in the presence of tyrosinase.37 48 Similar spectroscopic features were observed when the oxidations were carried out with lead dioxide in sulfuric acid solutions (pH> 1). If the initial oxidation was carried out for a short period of time, it was possible to regenerate the original catecholamines by reduction (e.g. with sodium bisulfite, potassium iodide, and zinc powder) and to show that the 385 mp peak disappeared.77,78 Kodja and Bouchilloux were also able to identify 2,4-dinitrophenylhydrazones of several of the intermediate non-cyclized quinones by paper chromatography and spectroscopy (Amax n weakly acid solution ca. 350 mp with a shoulder at ca. 410 mp).77,78... 

The ICD of the dyes bound to saccharides through an ionic coupling or hydrophobic interaction may remain a conflicting problem. The side-chain chromophores covalently bound to saccharides permit CD bands in the far or near ultraviolet region. These side-chain chromophores can exhibit CD and thus provide more definitive information on the conformation of saccharide moieties. Thus, acetamide CD has been observed to reflect polymer secondary structure of glycosaminoglycans, which are the connective-tissue proteoglycans. 

---